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annotator
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Reverting back to the old definition of QD because it works better with large numbers of samples. The new QD is relegated to a new annotation: sumGLbyD. Tweaks to the new HaplotypeScore based on evaluation with better QD calculation. The default qual threshold in GenerateVariantClusters is updated to be in line with the variant quality scores coming from the exact model.
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2011-01-13 14:12:30 +00:00 |
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beagle
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There's no reason to special case no-calls if they already have PLs associated with them. Just use the PLs!
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2011-01-31 15:05:45 +00:00 |
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coverage
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Some basic integration tests detecting breakage in OTF BAM index generation.
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2011-01-26 23:48:04 +00:00 |
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fasta
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Changing testing framework from junit -> testng, for its enhanced configurability.
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2010-11-01 21:31:44 +00:00 |
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filters
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Remove the extra trailing tab at the end of the VCF ## header line. Unfortunately, this meant updating every freaking integration test.
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2010-12-08 17:22:29 +00:00 |
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genotyper
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added integration test for --sites_only option
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2011-01-26 14:58:15 +00:00 |
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indels
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Changing testing framework from junit -> testng, for its enhanced configurability.
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2010-11-01 21:31:44 +00:00 |
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phasing
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Remove the extra trailing tab at the end of the VCF ## header line. Unfortunately, this meant updating every freaking integration test.
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2010-12-08 17:22:29 +00:00 |
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qc
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Changing testing framework from junit -> testng, for its enhanced configurability.
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2010-11-01 21:31:44 +00:00 |
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recalibration
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Bug fix in CountCovariates, skip over indel records as well as SNPs in the dbsnp file. CountCovariates is now called CountCovariatesWalker. I've always hated that the name was swapped.
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2010-12-02 18:43:24 +00:00 |
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sequenom
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Updated integration test's MD5s reflect the fact that assay sequences were previously designed incorrectly for indels, the bug is now fixed.
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2011-01-28 23:00:22 +00:00 |
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varianteval
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Updates to VariantEval 3.0 integration test.
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2011-01-31 17:45:06 +00:00 |
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variantrecalibration
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Removed LibBat.SUB2_BSUB_BLOCK since the use of it exits the JVM.
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2010-12-14 19:57:20 +00:00 |
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variantutils
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<key>=<value> tagging support for command-line arguments. Unfortunately, still
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2011-01-21 00:22:42 +00:00 |
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BAQIntegrationTest.java
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Better query start / stop function that directly parses the cigar string, unlike the previous version. Now properly handles H (hard-clipped) reads. Added -baq OFF and -baq RECALCULATE integration tests on all three 1KG technologies. Please let me know if this new code somehow fails.
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2011-01-28 15:08:21 +00:00 |
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ClipReadsWalkersIntegrationTest.java
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Changing testing framework from junit -> testng, for its enhanced configurability.
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2010-11-01 21:31:44 +00:00 |
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PileupWalkerIntegrationTest.java
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Changing testing framework from junit -> testng, for its enhanced configurability.
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2010-11-01 21:31:44 +00:00 |
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PrintReadsWalkerUnitTest.java
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Changing testing framework from junit -> testng, for its enhanced configurability.
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2010-11-01 21:31:44 +00:00 |
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VariantsToVCFIntegrationTest.java
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Support for indels in hapmap. This was non-trivial because not only does hapmap not tell you whether the allele is an insertion or deletion, but it also has a completely different positioning strategy (rightmost base). I'll send out an email tomorrow when the new HapMap3.3 VCF is ready.
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2010-12-27 07:37:46 +00:00 |
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